Question

Bioconductor: quantile normalization

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KVC_bioinfo • 0

@kvc_bioinfo-15319

Last seen 6.1 years ago

Hello All,

I have used Bioconductor ‘preprocessCore’ fro quantile normalization. I am trying t understand how does it work with low expressed or zero count genes. Is someone aware of that? Does it remove the low expressed genes?

TIA

normalization quantile preprocesscore • 1.7k views

ADD COMMENT • link updated 6.1 years ago by James W. MacDonald 65k • written 6.1 years ago by KVC_bioinfo • 0

score 2 · Accepted Answer · 2018-03-22

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 1 day ago

United States

No, it doesn't remove anything. It wouldn't make any sense to do that. If you look at the help page for normalize.quantiles, there is a link to a pdf that explains the procedure.

That said, preprocessCore, and normalize.quantiles are intended for microarray measurements, and using for count data is probably suboptimal.

ADD COMMENT • link 6.1 years ago James W. MacDonald 65k

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Thank you very much. I have used that on RNA-seq counts

ADD REPLY • link 6.1 years ago KVC_bioinfo • 0

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Well, like I said, that is probably not what you want to do. There are established RNA-Seq analysis pipelines, such as DESeq2 and edgeR, which handle the normalization of the count data in a statistically defensible manner. Unless you know what you are doing, it's probably best to use existing tools rather than a hodgepodge of methods borrowed from various analysis pipelines.

ADD REPLY • link 6.1 years ago James W. MacDonald 65k